Cooperative and dynamic assembly of affinity complexes

Abstract

The invention generally relates to the field of immunochemistry including antibody therapy, diagnostics, and basic research and specifically relates to the area of alternatives to natural antibodies including artificial antibodies or antibody mimics. The invention relates particularly to the cooperative assembly of stable affinity complexes.

1 . An affinity complex composition comprising providing (a) two or more primary affinity molecules, wherein said primary affinity molecules have affinity for one or more target molecules; and (b) one or more linker affinity molecules, wherein said linker affinity molecules have affinity for two or more of said primary affinity molecules; wherein said linker affinity molecules form a bridge when bound to two or more of said primary affinity molecules. 
   
   
       2 . The affinity complex composition of  claim 1 , wherein said affinity complex composition preferentially assembles into a complex upon binding to a target molecule. 
   
   
       3 . The affinity complex composition of  claim 1 , wherein said primary affinity molecules are selected from the list of natural antibodies, antibody fragments, single chain variable fragments, Nanobodies, Affibodies, Anticalins, DARPins, Monobodies, Avimers, and Microbodies. 
   
   
       4 . The affinity complex composition of  claim 1 , wherein said primary affinity molecules are expressed from genes. 
   
   
       5 . The affinity complex composition of  claim 1 , wherein said two or more primary affinity molecules comprise the same type of affinity molecule. 
   
   
       6 . The affinity complex composition of  claim 1 , wherein said two or more primary affinity molecules comprise two or more types of affinity molecules. 
   
   
       7 . The affinity complex composition of  claim 1 , wherein said two or more primary affinity molecules bind to different epitopes on said target molecule. 
   
   
       8 . The affinity complex composition of  claim 1 , wherein said two or more primary affinity molecules bind to the same epitope on a target molecule. 
   
   
       9 . The affinity complex composition of  claim 8 , wherein said target is a homomultimer and said epitopes are discontinuous. 
   
   
       10 . The affinity complex composition of  claim 1 , wherein said linker affinity molecule comprises two or more secondary affinity domains that are linked. 
   
   
       11 . The affinity complex composition of  claim 10 , wherein said secondary affinity domains bind said primary affinity molecules at an epitope. 
   
   
       12 . The affinity complex composition of  claim 11 , wherein binding of said secondary affinity domains to said primary affinity molecules does not disrupt the function of said primary affinity molecules. 
   
   
       13 . The affinity complex composition of  claim 10 , wherein said secondary affinity domains of said linker affinity molecule are covalently attached by a flexible linker. 
   
   
       14 . The affinity complex composition of  claim 13 , wherein said flexible linker is selected from the list of polypeptide, a nucleic acid strand, polyethylene glycol, and peptide nucleic acid (PNA). 
   
   
       15 . The affinity complex composition of  claim 14 , wherein said secondary affinity domains and said flexible linker comprise a single polypeptide. 
   
   
       16 . The affinity complex composition of  claim 14 , wherein said secondary affinity domains and said flexible linker are attached through a non-covalent interaction. 
   
   
       17 . The affinity complex composition of  claim 1 , further comprising one or more accessory molecules. 
   
   
       18 . The affinity complex composition of  claim 17 , wherein said accessory molecules are selected from the list of fluorescent molecules, radioactive molecules, enzymes, inhibitors, drug molecules, and cell adhesion molecules. 
   
   
       19 . The affinity complex composition of  claim 17 , wherein said accessory molecules are bound to said linker affinity molecule or to one or more of said primary affinity molecules. 
   
   
       20 . The affinity complex composition of  claim 17 , wherein said accessory molecules comprise two or more fluorescent molecules linked to two or more affinity molecules. 
   
   
       21 . The affinity complex composition of  claim 20 , wherein FRET can be detected between said fluorescent molecules upon formation of said affinity complex composition. 
   
   
       22 . The affinity complex composition of  claim 17 , wherein said accessory molecules comprise a drug molecule, and wherein said drug molecule is incorporated into a cell upon interaction of said affinity complex composition with said target. 
   
   
       23 . The affinity complex composition of  claim 1 , wherein said linker affinity molecule comprises an affinity complex comprising two or more secondary affinity molecules, wherein said secondary affinity molecules have affinity for each other. 
   
   
       24 . The affinity complex composition of  claim 23 , wherein said secondary affinity molecules comprise coiled coil peptide sequences that interact in a specific manner. 
   
   
       25 . The affinity complex composition of  claim 23 , wherein said secondary affinity molecules comprise complementary nucleic acid sequences. 
   
   
       26 . The affinity complex composition of  claim 23 , wherein each said secondary affinity molecule has affinity for a tertiary affinity molecule. 
   
   
       27 . The affinity complex composition of  claim 26 , wherein binding of said tertiary affinity molecule to said secondary affinity molecules does not interfere with binding of said secondary affinity molecules to said primary affinity molecules. 
   
   
       28 . The affinity complex composition of  claim 23 , wherein said secondary affinity molecules interact with more than one domain of said primary affinity molecule. 
   
   
       29 . The affinity complex composition of  claim 1 , wherein said affinity complex composition comprises a tyrosine/serine binary-code interface. 
   
   
       30 . The affinity complex composition of  claim 1 , wherein said affinity complex composition comprises a tyrosine/serine/X amino acid tertiary-code interface. 
   
   
       31 . The affinity complex composition of  claim 1 , wherein the interaction of a paratope of said primary affinity molecule to an epitope of said target molecule causes a change in the conformation of the primary affinity molecule to increase affinity of the linker interaction domain with the linker affinity molecule. 
   
   
       32 . The affinity complex composition of  claim 1 , wherein standard cellular process causes a change in the conformation of said primary affinity molecule to increase the affinity of its linker interaction domain with said linker affinity molecule. 
   
   
       33 . The affinity complex composition of  claim 32 , wherein said standard cellular process comprises: a protease, kinase, or phosphatase reaction; or a metal binding event. 
   
   
       34 . The affinity complex composition of  claim 1 , wherein said affinity complex composition comprises three primary affinity molecules, wherein each of said primary affinity molecules bind to discontinuous epitopes of said target, and wherein said linker affinity molecules binds to said primary affinity molecules through secondary affinity molecules.